Hi Thomas -
Probably having a single BioSQLSequenceDB on the central appserver is the
way to go as long as everything is synchronized. Ihave to say the client
server idea sounds good though. Could possible make a SessionBean that
looks like a SequenceDB, let the server sort out all the transaction
control! I might play with that idea for a while and see how it works.
- Mark
Thomas Down <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
05/21/2004 04:34 PM
To: Mark Schreiber/GP/[EMAIL PROTECTED]
cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] BioSQL transaction control
On 21 May 2004, at 06:55, [EMAIL PROTECTED] wrote:
> Hi -
>
> I'm going to start using BioSQL fairly intensively soon and I was
> wondering at what level the biojava bindings to biosql control
> transactions. Specifically: if I get a reference to a Sequence object
> from
> my SequenceDB does that reference lock the underlying entry (entries)
> in
> the database or does it just give me a local copy to play with and then
> release the lock on the DB?
Neither.
The code supports lazy loading, otherwise it would be easy to make it
explode on anything remotely resembling a large sequence, so the
Sequence objects you get back are dependent on the database. On the
other hand, the schema is too complex to realistically consider
"locking" a sequence. So you should only really have one
BioSQLSequenceDB accessing a database at a given time.
If you need multiple applications accessing the database at once, can
you put them all in a single appserver so that they can share a single
BioSQLSequenceDB? Otherwise, reasonable options are:
- Having one server export an object-oriented view of the
BioSQLSequenceDB to other application (Corba/SOAP/RMI/whatever).
[Aside: it would be really nice to have some kind of client-server view
on BioJava. If this was biojava-specific rather than trying to make it
an interoperability point (like BioCorba/bsane/etc.) it might actually
be usable]
- When you need a sequence, lock the database, get the sequence out
of BioSQL, copy it into an in-memory object, then release the lock.
- Hack the BioSQL code to disable lazy loading.
Without knowing a lot more about your applications, I'm not really in a
position to say which of these are more appropriate.
Thomas.
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